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zhongzhd / ont_m6a_detection

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Questions about the ont_m6a_detection procedures #8

Closed ShelaLJJ closed 12 months ago

ShelaLJJ commented 1 year ago

Hello, thank you all for developing this tool!

I am a little bit confused about the procedure about using the scripts from ont_m6a_detection. Since the published DRS datasets derived from WT and Mettl3 KO mESC samples [SRP166020] have huge size, I am finding test data to run through the whole process. I noticed that your paper mentioned "GSE195618" and it has all the bed files, are these bed files generated from the 2nd step "m6A detection"? Should I continue to use these bed files in the 3rd step "postprocess"?

And do you have any tools that can produce the "txt=path_to_transcript_list" in DRUMMER.sh (m6A detection step)?

Appreciate it a lot if you could help answer these questions! Best, Shela

zhongzhd commented 12 months ago

I'm sorry, I've been very busy and couldn't reply to messages in a timely manner. The bed files in "GSE195618" are not the results from the 2nd step "m6A detection", but the results from all tools with default paremeters. Can you give me your email address? I can directly send you the source data. "txt=path_to_transcript_list" in DRUMMER.sh can easily extracted by awk.

ShelaLJJ commented 12 months ago

Hi,

Thanks for your reply! It would be great if you can share me the source data.

And may I ask from what file can I extract the path_to_transcript_list?

Best regards